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Metagenomic analysis
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Binh Chau hot spring locates in Bung Rieng commune, Xuyen Moc district, Ba Ria - Vung Tau province, and is the second hottest hot spring in Vietnam. Up to date, the microbial diversity of this hot spring has been mainly evaluated using the culture-dependent methods, thus, it could not be able to assess all of microorganisms there.
11p
vimulcahy
18-09-2023
5
3
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Metagenomics allows us to acquire the potential resources from both cultivatable and uncultivable microorganisms in the environment. Here, shotgun metagenome sequencing was used to investigate microbial communities from the surface layer of low grade copper tailings that were industrially bioleached at the Dexing Copper Mine, China.
12p
vinarcissa
21-03-2023
4
1
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In order to determine the role of the database in taxonomic sequence classification, we examine the influence of the database over time on k-mer-based lowest common ancestor taxonomic classification. We present three major findings: the number of new species added to the NCBI RefSeq database greatly outpaces the number of new genera; as a result, more reads are classified with newer database versions, but fewer are classified at the species level; and Bayesian-based re-estimation mitigates this effect but struggles with novel genomes.
10p
vigalileogalilei
27-02-2022
11
1
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The MinHash algorithm has proven effective for rapidly estimating the resemblance of two genomes or metagenomes. However, this method cannot reliably estimate the containment of a genome within a metagenome. Here, we describe an online algorithm capable of measuring the containment of genomes and proteomes within either assembled or unassembled sequencing read sets.
13p
vielonmusk
30-01-2022
14
0
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Although Kraken’s k-mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves upon Kraken 1 by reducing memory usage by 85%, allowing greater amounts of reference genomic data to be used, while maintaining high accuracy and increasing speed fivefold.
13p
vielonmusk
30-01-2022
9
0
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Humans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide a better understanding of the human microbiome. Comparative metagenomic analysis of human and non-human primate (NHP) microbiomes offers a promising approach to study this symbiosis.
16p
vielonmusk
30-01-2022
58
0
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Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data.
21p
vialfrednobel
29-01-2022
9
0
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High-throughput sequencing enables unbiased profiling of microbial communities, universal pathogen detection, and host response to infectious diseases. However, computation times and algorithmic inaccuracies have hindered adoption.
18p
viaristotle
29-01-2022
9
0
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The correct identification of differentially abundant microbial taxa between experimental conditions is a methodological and computational challenge. Recent work has produced methods to deal with the high sparsity and compositionality characteristic of microbiome data, but independent benchmarks comparing these to alternatives developed for RNA-seq data analysis are lacking.
31p
viarchimedes
26-01-2022
11
2
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Microbial eukaryotes constitute a significant fraction of biodiversity and have recently gained more attention, but the recovery of high-quality metagenomic assembled eukaryotic genomes is limited by the current availability of tools. To help address this, we have developed EukCC, a tool for estimating the quality of eukaryotic genomes based on the automated dynamic selection of single copy marker gene sets.
21p
viarchimedes
26-01-2022
6
0
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Metagenomic profiling, predicting the presence and relative abundances of microbes in a sample, is a critical first step in microbiome analysis. Alignment-based approaches are often considered accurate yet computationally infeasible. Here, we present a novel method, Metalign, that performs efficient and accurate alignmentbased metagenomic profiling.
15p
viarchimedes
26-01-2022
13
0
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Microbiome meta-analysis and crossdisease comparison enabled by the SIAMCAT machine learning toolbox
The human microbiome is increasingly mined for diagnostic and therapeutic biomarkers using machine learning (ML). However, metagenomics-specific software is scarce, and overoptimistic evaluation and limited cross-study generalization are prevailing issues.
27p
viarchimedes
26-01-2022
14
0
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Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been carried out.
27p
viarchimedes
26-01-2022
15
1
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The present study applied metagenomics to characterize the diversity and relative occurrence of eukaryotic organisms in the sea water (LC05.W and LCDN.W) and sediment (LC05.S and LCDN.S) samples collected at the Lang Co - Da Nang sea in two years 2016 and 2017. The marine DNA metagenomes from water and sediments were isolated and analyzed by using specific primer 18S V4: 528F-706R with the barcode for gene-based metagenomic approach.
11p
vielonmusk
21-01-2022
20
0
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The main objective of this study was to estimate the taxonomic diversity of microbial species present in ready-toeat ceviche using a metagenomic approach. Six samples of commercially available ceviche were subjected to DNA high throughput sequencing and bioinformatics analyses, we identified between 65,000 and 131,000 reads per sample. The predominant phyla identified through the samples were Proteobacteria, Bacteroidetes and Firmicutes.
5p
mudbound
10-12-2021
8
1
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Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Although tools for this purpose exist for 16S ribosomal RNA sequencing analysis, there is a growing but still insufficient number of user-friendly interactive visualization workflows for easy data exploration and figure generation. The development of such platforms for this purpose is necessary to accelerate and streamline microbiome laboratory research.
11p
vibeauty
23-10-2021
10
1
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In shotgun metagenomics, microbial communities are studied through direct sequencing of DNA without any prior cultivation. By comparing gene abundances estimated from the generated sequencing reads, functional differences between the communities can be identified. However, gene abundance data is affected by high levels of systematic variability, which can greatly reduce the statistical power and introduce false positives. Normalization, which is the process where systematic variability is identified and removed, is therefore a vital part of the data analysis.
17p
vibeauty
23-10-2021
10
2
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Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. Recently, traditional isolation methods, complemented by high-throughput sequencing metagenomics technology, have greatly increased our understanding of the diversity of bacteriophages. Oceanospirillum, within the order Oceanospirillales, are important symbiotic marine bacteria associated with hydrocarbon degradation and algal blooms, especially in polar regions.
16p
vitzuyu2711
29-09-2021
6
1
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Prosthetic joint infections are clinically difficult to diagnose and treat. Previously, we demonstrated metagenomic sequencing on an Illumina MiSeq replicates the findings of current gold standard microbiological diagnostic techniques. Nanopore sequencing offers advantages in speed of detection over MiSeq.
11p
vitzuyu2711
29-09-2021
7
1
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Numerous protocols for viral enrichment and genome amplification have been created. However, the direct identification of viral genomes from clinical specimens using next-generation sequencing (NGS) still has its challenges. As a selected viral nucleic acid extraction method may determine the sensitivity and reliability of NGS, it is still valuable to evaluate the extraction efficiency of different extraction kits using clinical specimens directly.
8p
vitzuyu2711
29-09-2021
4
1
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